While the water quality of many European streams improves, sediments as sinks and secondary pollutant sources are underestimated by the European Water Framework Directive. Extreme flood events like the Elbe flood of August 2002 pose a risk to remobilize sediment particle bound persistent organic pollutants (POP) that can endanger wild life and even human beings. The aim of the present study was to compare the dioxin-like activity of Elbe sediments from the year 2008 and soil samples of the Elbe associated flood area, sampled after the Elbe flood of August 2002. This study shows the importance of ecotoxicological sediment assessment, especially in times of climatic change and increasing flood events. It also clearly shows evidence that chemical investigations can underestimate the toxic potential of sediments due to missing data of non-classical AhR-inducers. As a consequence, bioanalytical endpoints should also be considered when assessing the toxicity of complex environmental samples.